Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations

Donna M. Toleno, Peter L. Morrell, Michael T. Clegg

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Motivation: Errors in nucleotide sequence and SNP genotyping data are problematic when inferring haplotypes. Previously published methods for error detection in haplotype data make use of pedigree information; however, for many samples, individuals are not related by pedigree. This article describes a method for detecting errors in haplotypes by considering the recombinational history implied by the patterns of variation, three SNPs at a time. Results: Coalescent simulations provide evidence that the method is robust to high levels of recombination as well as homologous gene conversion, indicating that patterns produced by both proximate and distant SNPs may be useful for detecting unlikely three-site haplotypes.

Original languageEnglish (US)
Pages (from-to)1807-1814
Number of pages8
JournalBioinformatics
Volume23
Issue number14
DOIs
StatePublished - Jul 15 2007

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